biotite.structure.alphabet#

A subpackage for converting structures to structural alphabet sequences.

Structural alphabets represent the local geometry of each residue in a structure as symbol in a sequence. This allows using sequence-based functionality from biotite.sequence on structural data.

For each supported structural alphabet, this subpackage provides a conversion function that converts each chain of a given structure into a Sequence object from the respective structural alphabet.

Note that the structural alphabets use lower-case letters as symbols, in order to distinguish them better from the nucleotide and amino acid alphabets.

Structural alphabets#

I3DSequence

Representation of a structure in the 3Di structural alphabet.

ProteinBlocksSequence

Representation of a structure in the Protein Blocks structural alphabet.

Conversion Function#

to_3di

Encode each chain in the given structure to the 3Di structure alphabet.

to_protein_blocks

Encode each chain in the given structure to the Protein Blocks structural alphabet.